Supplemental tables
Suppl. Table 1: Distribution of the distinct T-DNA and Tos17 insertion loci of the OTL library among the 12 rice chromosomes and number
and % of inserts in the coding sequence compartment of predicted genes residing on these chromosomes.
Chr.
1
2
3
4
5
6
7
8
9
10
11
12
Size (bp)
43268879
35930381
36406689
35278225
29894789
31246789
29696629
28439308
23011239
23134759
28512666
27497214
Total
2504
1888
2112
1435
1229
1333
1241
1174
962
885
1018
1033
Locus T-DNA
Exon+Intron
621
495
530
349
299
325
314
322
236
214
279
280
%
24,8
26,2
25,1
24,3
24,3
24,4
25,3
27,4
24,5
24,2
27,4
27,1
Total
1552
1691
1352
1148
1014
1119
1024
963
662
580
569
737
Locus Tos17
Exon+Intron
1182
1428
1004
881
723
817
608
680
442
422
400
570
%
76,2
84,4
74,3
76,7
71,3
73,0
59,4
70,6
66,8
72,8
70,3
77,3
Total
4056
3579
3464
2583
2243
2452
2265
2137
1624
1465
1587
1770
Total
Exon+Intron
1803
1923
1534
1230
1022
1142
922
1002
678
636
679
850
%
44,5
53,7
44,3
47,6
45,6
46,6
40,7
46,9
41,7
43,4
42,8
48,0
Total
372317567
16814
4264
25,4
12411
9157
73,8
29225
13421
45,9
From Miyao et al 2007
Total lines From Chern et al 2007
Number of traits : 53
Category
Sub-category
50000
Total lines This study
Number of traits : 61
# lines
Freq
Category
Sub-category
Growth
Germination rate
22,665
# lines
Freq
Category
Sub-category
1
0,00
Germination
Germination rate
Growth
1 Germination
Low germination rate
3489
6,98
2 Growth
Lethal
1630
3,26
Lethal
139
0,61
Abnormal shoot
1787
3,57
Abnormal plants
10
0,04
Weak
1607
3,21
Weak
105
0,46
Albino
1407
2,81
Albino
13
0,06
Yellow
810
1,62
Yellow leaf
21
Dark green
1065
2,13
Dark green leaf
Pale green
1732
3,46
Virescent
834
Stripe
Zebra
3 Leaf color
4 Leaf shape
Total lines
Number of traits : 71
Freq
6108
21,95
Lethal
560
2,01
Abnormal plants
210
0,75
Weak
286
1,03
Albino
186
0,67
0,09
Yellow leaf
653
2,35
931
4,11
Dark green leaf
29
0,10
Pale green leaf
286
1,26
Pale green leaf
19
0,07
1,67
Bluish green leaf
69
0,30
Virescent
4
0,01
397
0,79
Stripe
46
0,20
Stripe
254
0,91
109
0,22
Zebra
7
0,03
Zebra
17
0,06
Stay green
2
0,01
Others
3
0,01
Wide leaf
92
0,33
Others
85
0,17
Wide leaf
143
0,29
Narrow leaf
1379
Long leaf
Leaf color
Leaf color
Others
159
0,70
Wide leaf
186
0,82
2,76
Narrow leaf
1119
4,94
Narrow leaf
48
0,17
30
0,06
Long leaf
370
1,63
Long leaf
87
0,31
Short leaf
40
0,08
Short leaf
540
2,38
Short leaf
32
0,11
Drooping leaf
227
0,45
Drooping leaf
66
0,29
Drooping leaf
32
0,11
Rolled leaf
343
0,69
Rolled leaf
550
2,43
Rolled leaf
88
0,32
Spiral leaf
111
0,22
Spiral leaf
323
1,43
Spiral leaf
18
0,06
Brittle leaf/culm
124
0,25
Brittle leaf/culm
14
0,06
Brittle leaf/culm
14
0,05
Abnormal lamina joint angle
96
0,19
Thin lamina joint
5
0,02
Withering
888
1,78
Withering
160
0,71
Leaf morphology
Leaf morphology
Horizontal leaf
5 Culm shape
27832
#l ines
Others
346
0,69
Semi-dwarf
3670
7,34
Dwarf
5722
Severely dwarf
Long culm
330
1,19
Erect leaf
69
0,25
Others
64
0,23
Semidwarf
847
3,04
Others
127
0,56
Semidwarf
872
3,85
11,44
Dwarf
1242
5,48
Dwarf
250
0,90
1376
2,75
Extremely dwarf
111
0,49
Long culm
136
0,49
679
1,36
Long culm
24
0,11
Erect
5
0,02
Erect
194
0,86
Spread-out
104
0,37
Spread-out
413
1,82
Thin culm
21
0,08
Plant morphology
Plant morphology
Fine culm
18
0,04
Thin culm
873
3,85
Thick culm
24
0,09
Thick culm
63
0,13
Thick culm
21
0,09
Lazy
28
0,10
Lazy
376
0,75
Lazy
1
0,00
Compact
90
0,32
7
0,03
Culm branching
Others
8
0,02
1102
2,20
Mimic response
Lesion mimic
258
1,14
Mimic response
Lesion mimic
273
0,98
High tillering
111
0,22
Tiller
High tiller position
8
0,04
Tiller
High tillering
79
0,28
Low tillering
2837
5,67
Low tiller position
0
0,00
Low tillering
167
0,60
Monoculm
74
0,33
Monoculm
35
0,13
Few panicle
352
1,55
Many panicle
1092
4,82
Early heading
14
0,06
6 Spotted leaf/lesion mimic Spotted leaf/lesion mimic
7 Tillering
8 Heading date
9 Spikelet
10 Panicle
Early heading
1797
3,59
Early heading
0
0,00
Late heading
1244
2,49
Late heading
195
0,86
Late heading
401
1,44
Non-heading
96
0,19
No heading
140
0,62
No heading
0
0,00
Abnormal hull
508
1,02
Abnormal hull
38
0,17
223
0,80
Abnormal floral organ
211
0,42
Abnormal floral organ
1
0,00
Abnormal floral organ
0
0,00
With awn
36
0,16
Awned
106
0,38
Abnormal hull
9
0,04
Abnormal hull color
91
0,40
Heading date
Flower
Heading date
Flower
Abnormal hull
52
0,19
Others
3
0,01
Long panicle
4
0,01
Abnormal hull color
Panicle morphology
Long panicle
29
0,06
Panicle morphology Long panicle
35
0,15
Short panicle
752
1,50
Short panicle
939
4,14
Short panicle
4
0,01
Lax panicle
104
0,21
Sparse panicle
270
1,19
Sparse panicle
0
0,00
Dense panicle
264
0,53
Dense panicle
189
0,83
Dense panicle
28
0,10
Viviparous
1105
2,21
Viviparity
0
0,00
Shattering
6
0,01
Shattering
5
0,02
Shattering
0
0,00
Neck leaf
171
0,34
Neck leaf
36
0,16
Neck leaf
0
0,00
Abnormal panicle shape
433
0,87
Abnormal panicle shape 178
0,79
Abnormal panicle shape
120
0,43
Incomplete exertion
27
0,10
Few spikelets
40
0,14
8
0,03
Others
49
0,18
Seed fertility
Sterile
1311
4,71
Seed morphology
Terminal spikelet
11 Sterility
12 Seed
Seed fertility
Others
173
0,76
Sterile
571
2,52
Low fertility
403
1,78
Sterile
3825
7,65
Low fertility
12542
25,08
Large grain
195
0,39
Large grain
29
0,13
Large grain
0
0,00
Small grain
427
0,85
Small grain
1063
4,69
Small grain
71
0,26
Slender grain
101
0,20
Slender grain
29
0,13
Slender grain
0
0,00
Others
3469
6,94
Others
64
0,28
Others
0
0,00
22
0,08
Seed morphology
Root system
Weak root
Suppl. Table 2: Correspondence between categories and sub categories of traits observed in previous field evaluations of Nipponbare NIAS
Tos17 lines (Miyao et al., 2007) and Tainung67 TRIM T-DNA activation tagging lines (Chern et al., 2007) with those of this study
Suppl. Table 3: Frequency of occurrence of the altered traits in the OTL library according to the
Trait Ontology categories.
TO code
TO:0000430
TO:0000436
TO name
germination rate
spikelet sterility
TO:0000464
TO:0000576
TO:0000326
TO:0000207
albino plantlet
differentiation
frequency
stem length
leaf color
plant height
TO:0000344
days to flower
TO:0000206
leaf angle
TO:0000369
vegetative
growth time
variegated leaf
tiller number
TO:0000069
TO:0000346
TO:0002714
TO:0000492
TO:0000657
TO:0000370
TO:0000063
TO:0000567
TO:0000072
TO:0000560
TO:0000050
plastid
development
trait
leaf shape
spikelet anatomy
and morphology
trait
leaf width
TO:0000124
mimic response
tiller angle
awn length
space per culm
inflorescence
branching
flag leaf angle
TO:0000652
leaf necrosis
TO:0000089
panicle type
TO:0000240
sterile lemma
length
spikelet length to
width ratio
glume color
leaf thickness
ear number
TO:0000563
TO:0000221
TO:0000258
TO:0000443
TO definition
Rate of germination of the seed.
Determined by counting the filled and unfilled spikelets of
the bagged grass inflorescence.
[No definition available]
# lines
6108
1311
Frequency
21.95
4.71
745
2.68
Length of the stem.
Changes observed in the color of leaf.
Actual measurement of plant height from soil surface to
the highest point in plant as identified in the study.
Number of days from the seed sowing or the seedling
transplant date (in some cases of rice) to the anthesis
(flowering) stage.
The angle of openness of the blade tip is measured against
the stem.
Measure of the vegetative growth phase time in a plant's
life cycle.
[No definition available]
Number of tillers per plant, should represent most plants
within a study.
Trait(s) associated with phenotypes observed for abnormal
development of plastid structure and its biogenesis.
726
724
482
2.61
2.60
1.73
401
1.44
356
1.28
286
1.03
263
255
0.94
0.92
206
0.74
Variation in shapes and forms of leaf.
Traits associated with changes in the anatomy or structure
of the spikelet and its parts.
158
152
0.57
0.55
Actual measurements, in centimeters of the widest portion
of the leaf. To be precise use the children terms leaf
lamina width (TO:0002720) or 'leaf sheath width
(TO:0002721).
[No definition available]
[No definition available]
Defines the length of awn.
Space occupied by each culm or the tiller in a plant.
The extent of branching usually sets the tone for shape and
compactness of the inflorescence.
In grasses the flag leaf angle is measured near the collar as
the angle of attachment between the flag leaf blade and the
main inflorescence axis in grass plants.
Leaf surface area affected by abiotic stresses like
insecticides and cold temperature as evidenced by
chlorotic and/or necrotic tissue.
Panicle types are classified according to their mode of
branching, angle of primary branches, and spikelet
density.
Length of the sterile lemma. The measurement is made on
each of the two sterile lemmas.
A ratio of length to the width of the spikelet.
135
0.49
134
132
106
90
89
0.48
0.47
0.38
0.32
0.32
74
0.27
62
0.22
58
0.21
51
0.18
50
0.18
Color of the glume.
[No definition available]
Number of ears found in a plant or and average number
present in population.
47
47
40
0.17
0.17
0.14
TO:0000027
culm number
TO:0000070
variegated leaf
necrosis
TO:0000040
panicle length
TO:0000361
TO:0000165
stem anatomy
and morphology
trait
panicle exsertion
TO:0000019
seedling height
TO:0000051
TO:0000108
stem strength
leaf shattering
TO:0000201
TO:0000198
TO:0000614
TO:0000135
TO:0000470
panicle color
rootless
lemma shape
leaf length
vascular tissue
related trait
panicle shape
brittle culm
leaf number
stem thickness
pedicel length
seed length
TO:0000262
TO:0000200
TO:0000241
TO:0000339
TO:0000630
TO:0000146
TO:0000545
TO:0000708
TO:0000404
TO:0000474
panicle base to
lowest branch
panicle number
leaf development
trait
leaf elongation
rate
plant color
nodal rooting
glume opening
TO:0000469
days to maturity
TO:0002712
stay green trait
TO:0000446
TO:0000419
TO:0000250
TO:0000190
TO:0002722
leaf drying
leaf anatomy and
morphology trait
vigor related trait
seed coat color
leaf pubescence
TO:0000024
ligule length
TO:0000249
leaf senescence
TO:0000534
culm color
TO:0000152
TO:0000655
TO:0000360
Actual count of the total number of tillers after full
heading, Specify if per plant, hill or area
Variegated leaf necrosis or scorching observed in response
to stresses like drought, insecticides and cold temperature
as evidenced by chlorotic and/or necrotic tissue.
Is the actual measurement in centimeters from panicle
base to tip.
Traits associated with changes in the anatomy or structure
of the stem and its parts.
35
0.13
33
0.12
31
0.11
28
0.10
Trait monitored by observing the extent of coverage of
panicle by the flag leaf sheath.
Average height measurements of 10 seedlings, in
centimeters from the base of the shoot to the tip of the
tallest leaf blade.
The test gives indication of culm stiffness and resilience
Extent of leaf shattering based on the development of
abscission zone.
Variation in color of the panicle inflorescence.
Absence of roots in the seedling or plant
Shape of the lemma in a floret.
Actual measurements, in centimeters of the leaf.
Traits associated with changes in the anatomy or structure
of the vascular tissue and its parts.
Shape of the panicle inflorescence
A measure of brittleness of the stem of a grass plant.
Number of leaves in a plant at a particular growth stage
Thickness of the stem.
Length of the pedicel.
Is the average length of the seed or caryopsis fruit in a
cereal (with hull).
Length of the region between the panicle base to the
lowest (the first) primary panicle branch.
Average number of panicles per plant in a study.
Traits associated with observing effects on the
development of the leaf and its parts.
Measure of growth or elongation rate of the leaf in a plant.
27
0.10
25
0.09
24
23
0.09
0.08
22
22
20
20
15
0.08
0.08
0.07
0.07
0.05
15
14
13
12
12
9
0.05
0.05
0.05
0.04
0.04
0.03
8
0.03
8
5
0.03
0.02
5
0.02
The color of the plant.
Extent of rooting from the nodes on a stem.
Angle of opening of glumes is measured on each floret,
assessment based on mean angle of glume opening.
Number of days required from seeding to seed/grain
ripening.
The color of plant and the photosynthetic organs remain
green compared to turning yellow and or brown at the
time of senescing.
[No definition available]
Traits associated with changes in the anatomy or structure
of the leaf and its parts.
[No definition available]
The color of the seed coat
Extent of pubescence (presence of hairs) on the leaf
surface.
The actual measurement of ligules measured in
millimeters from the base of the leaf collar to the ligule
tip.
A measure of aging of leaf. Rapid senescence of leaves
can be detrimental to yield.
Variation in the color of the culm of a grass plant.
4
4
4
0.01
0.01
0.01
3
0.01
2
0.01
2
2
0.01
0.01
1
1
1
0.00
0.00
0.00
1
0.00
1
0.00
1
0.00
Suppl. table 3 (Ctd)